Additional file 3.

Additional analyses carried out to test the effects of SNP calling parameters, verify
called SNPs and to simulate the four-haplotypes test. Additional analyses carried out to test the effects of varying the SNP calling parameters
on the numbers of SNPs called in the Rahman strain, verify the called SNPs in Rahman
strain by comparison with an independently generated dataset and to simulate the four-haplotypes
test under models of varying recombination and gene conversion.